3D Structure Viewer

3D Structure Viewer

RxCubed opens saved PDB and mmCIF coordinate files in the Mol* 3D viewer. The viewer is read-only: it changes how you inspect a structure, not the saved evidence or its provenance.

Open a structure

1. Open Results Hub and select the saved coordinate file, not only the structure's metadata card.
2. Confirm that the viewer header identifies the expected structure, such as 3HS4.
3. Wait for the structure to load before using the controls. The sequence panel is above the 3D canvas and Structure Tools is on the right.

Navigate the structure

• Drag in the 3D canvas to rotate.
• Use the mouse wheel or trackpad to zoom.
• Click a component name in the Components panel to focus the camera on it.
• Click a residue in the sequence panel or on the structure to focus on that residue and its local surroundings.

Components and visibility

The Components panel commonly includes Polymer, Ligand, Water, and Ion. The component name and the eye icon do different things:

• Click the component name or row to focus it.
• Click the eye icon to show or hide that component. It does not focus the component.
• Use the options menu for a component to change its representation or colour.

To inspect a binding pocket, keep Polymer visible and click Ligand to focus the bound ligand. Do not hide Polymer or Ion with the eye icons. Click Ion only when you want to focus on the metal ion, then click Ligand again to return to the pocket view.

Example: 3HS4

For the tutorial structure 3HS4:

1. Click the Ligand row and inspect the bound acetazolamide ligand, whose PDB component code is AZM.
2. Keep the polymer visible so the active-site pocket remains understandable.
3. Use the nearby Ion component to inspect the zinc ion, then return focus to Ligand and rotate or zoom around the ligand--zinc pocket.

The panel may show a generic category such as “Ligand” or “Ion” rather than the component code. In that case, use the selected object in the canvas or sequence panel and the evidence Details view to confirm its identity.

If part of the structure disappears

You probably clicked an eye icon. Click that eye again to restore visibility, or choose a standard Polymer & Ligand preset if the viewer offers one. Keep the polymer visible when learning where a ligand or ion sits in its pocket.